On Wed, Jun 29, 2016, Slava Chushak wrote:
> Here is a nab script:
>
> molecule m;
> string seq;
> seq = "ATGGCCAATG";
> m = link_na("1", seq, "", "DNA", "35");
> putpdb( "DNA.pdb", m );
>
> Got an error message "Residue T not in library nab10.lib."
Wow...I'm guessing no one has used link_na() in this way for half a decade or
so. The code is using a old,old,old way of distinguishing between DNA
and RNA, back from the days when the PDB itself didn't distinguish between
A and DA (calling both "ADE").
See the attached patch file: there are only three lines to be added, so
you can do this by hand, or do this:
cd $AMBERHOME
patch -p0 < link_na.patch
In either case, type "make install in the $AMBERHOME/AmberTools/src/nab
directory.
This works for me for you example above. Also works for RNA (changing T
to U). Let me know if you find problems. I'll post an update soon.
Thanks for the report.
....dac
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Received on Wed Jun 29 2016 - 19:00:02 PDT
